Gerstein M, Lynden-Bell R M
MRC Laboratory of Molecular Biology Hills Road, Cambridge, U.K.
J Mol Biol. 1993 Mar 20;230(2):641-50. doi: 10.1006/jmbi.1993.1175.
At what distance do proteins in solution interact? Molecular simulation of water around two helices is used to address this question. Calculations are done with two ideal, parallel, polyalanine alpha-helices separated by 9 A, 11 A, 13 A, and 15 A. The second peak in the oxygen density (or loosely the second shell of water molecules) is used to define a hydration surface around the protein, which separates bulk solvent from water molecules strongly influenced by the protein. The hydration surface is contrasted with the Richards-Connolly molecular surface. It indicates that the helices are not completely separate until 15 A, while the molecular surface shows complete separation at 13 A. Suggesting shape-dependent aspects of hydration, the hydration surface only loosely follows the van der Waals outline of the protein surface. In particular, at the 9 A separation, the van der Waals envelopes of the helices make contact; two narrow crevices are formed on either side of the contact; and the water within the crevices is strongly localized in arrangements bridging the helices. A comparison of these 'normal' water simulations with a simulation of a simple, uncharged solvent highlights the importance of hydrogen bonding in structuring liquid water and further contrasts the molecular surface and the hydration surface.
溶液中的蛋白质在多大距离时会相互作用？围绕两条螺旋的水的分子模拟被用于解决这个问题。计算是用两条理想的、平行的聚丙氨酸α螺旋进行的，它们之间的间距分别为9埃、11埃、13埃和15埃。氧密度的第二个峰值（或大致上水分子的第二个壳层）被用来定义蛋白质周围的水合表面，该表面将本体溶剂与受蛋白质强烈影响的水分子分隔开来。将水合表面与理查兹-康诺利分子表面进行对比。结果表明，直到间距为15埃时螺旋才完全分开，而分子表面在13埃时就显示出完全分开。水合表面仅大致遵循蛋白质表面的范德华轮廓，这表明了水合作用中与形状相关的方面。特别是，在间距为9埃时，螺旋的范德华包络相互接触；在接触点的两侧形成了两条狭窄的裂缝；裂缝内的水在连接螺旋的排列中强烈地局部化。将这些“正常”水模拟与一种简单的不带电溶剂的模拟进行比较，突出了氢键在构建液态水结构中的重要性，并进一步对比了分子表面和水合表面。
